diff --git a/docs/options.sgml b/docs/options.sgml index 19934f80748ee5aed1b1b9e8cd613115b233f7d7..5543bf5005d2ba5e57c10398c71cfd3fdc665a18 100644 --- a/docs/options.sgml +++ b/docs/options.sgml @@ -400,6 +400,39 @@ gc_content_default_window_size = 150 See also <XREF LINKEND="GRAPHS">. </PARA> </SECT2> + + <SECT2 ID="OPTIONS-CHADO"> + <TITLE>Options For A Chado Database</TITLE> + + <SECT3 ID="OPTIONS-CHADO-EXON-MODEL"> + <TITLE><LITERAL>chado_exon_model</LITERAL></TITLE> + <PARA> + This is the feature key used when chado exons are joined and displayed in &prog;. + For example: <SYNOPSIS>chado_exon_model=CDS</SYNOPSIS> + [default: "exon-model"] + </PARA> + </SECT3> + + <SECT3 ID="OPTIONS-CHADO-TRANSCRIPT"> + <TITLE><LITERAL>chado_transcript</LITERAL></TITLE> + <PARA> + This is the feature key used when chado transcripts are created in a gene + model. [default: "mRNA"] + </PARA> + </SECT3> + + <SECT3 ID="OPTIONS-CHADO-SERVERS"> + <TITLE><LITERAL>chado_servers</LITERAL></TITLE> + <PARA> + This can be used to provide a list of available databases. For example: + <SYNOPSIS>chado_servers = \ + test localhost:5432/test?userName \ + genedb_ro db.genedb.org:5432/snapshot?genedb_ro + </SYNOPSIS> + </PARA> + </SECT3> + + </SECT2> </SECT1> <SECT1 ID="OPTIONS-FILE">